# SOAP format
#time ./gsnp -i /lhome/mian/data/chr21.soap.sort -d /home/luo_group/data/snp_data/human/hg18_ref/chr21.fa -o /lhome/mian/data/chr21.cns -M /lhome/mian/data/chr21.mat -u -t -L 100 -s /home/luo_group/data/snp_data/human/dbSNP/dbSNP.chr21.sort -2 -C

#GAligner format chr 21
#time ./gsnp -i /lhome/mian/data/chr21.soap.bin -d /home/luo_group/data/snp_data/human/hg18_ref/chr21.fa -o /lhome/mian/data/chr21.cns -M /lhome/mian/data/chr21.mat -u -t -L 100 -s /home/luo_group/data/snp_data/human/dbSNP/dbSNP.chr21.sort -2 -c /lhome/mian/data/chr21.soap.sort.cmat -C -G


#GAligner format chr 1
time ./gsnp -i /lhome/mian/data/chr1.soap.bin -d /home/luo_group/data/snp_data/human/hg18_ref/chr1.fa -o /lhome/mian/data/chr1.cns -M /lhome/mian/data/chr1.mat -u -t -L 100 -s /home/luo_group/data/snp_data/human/dbSNP/dbSNP.chr1.sort -2 -c /lhome/mian/data/chr1.soap.random.cmat -C -G

